印度昌迪加尔市微生物技术研究所生物信息学课件srs

1、08-Aug-22Text-Based Searching1Text-Based SearchingLesson 3Bioinformatics Laboratory08-Aug-22Text-Based Searching2Topics to be CoveredWeb serversEMBnetNCBIDatabase interrogationSRSEntrezStringsearch08-Aug-22Text-Based Searching3EMBnet European Molecular Biology NetworkIn 1988 a network was establishe

2、d to link European laboratories that used puting and bioinformatics in molecular biology research.In each country a national node provides local puting servicesINN serves as Israels National Node08-Aug-22Text-Based Searching4Israel National NodeINN serves as Israels National NodeAuthorized by the Mi

3、nistry of Science in 1990. INN is located at the Biological Computing Unit, Weizmann Institute of Science. 08-Aug-22Text-Based Searching5Bioinformatics Units at UniversitiesIn Israel, in the mid 1990s Bioinformatics Units arose at Universities to serve local needsAt TAU 08-Aug-22Text-Based Searching

4、6Database InterrogationTwo ways to search databasesDatabase interrogation searches textual information contained in header sections of database entriesDatabase searching searches sequence information with sequence queries08-Aug-22Text-Based Searching7Database Interrogation Problem of EMBnetNo effect

5、ive way of interrogating all the resources together at a particular site, since formats differA research project was undertaken with EMBnet to address problems inherent in interfacing complex environments resulting in SRS sequence retrieval system, a network browser for databases in molecular biolog

6、y08-Aug-22Text-Based Searching8SRSSRS allows any flat file database to be indexed to any other.Powerful tool that allows users to formulate queries across a range of different database types via a single interface, without having to worry about underlying data structures, query languages, etc.Sequen

7、ce Retrieval System08-Aug-22Text-Based Searching9SRS List of Public SRS Servers 08-Aug-22Text-Based Searching10SRS List of Public SRS Servers 08-Aug-22Text-Based Searching11Searching SRS08-Aug-22Text-Based Searching12SRS Tutorial08-Aug-22Text-Based Searching13Search SRS Databases08-Aug-22Text-Based

8、Searching14SRS Standard Query Form08-Aug-22Text-Based Searching15SRS Standard Query Form08-Aug-22Text-Based Searching16SRS Extended Query Form08-Aug-22Text-Based Searching17NCBINational Center for BiotechnologyEstablished in 1988 and located at the campus of NIH as a subdivision of NLM (National Lib

9、rary of Medicine)Since 1992 one of NCBIs major tasks has been maintenance of GenBank08-Aug-22Text-Based Searching18EntrezEntrez allows retrieval of molecular biology data and bibliographic citations from NCBIs integrated databasesEntrez, unlike SRS, does not allow customization with an institutes pr

10、eferred databases08-Aug-22Text-Based Searching19EntrezMost records are linked to other records, within a given database and between databasesSequence databases are linked to the Medline databases so that one can move from paper to sequence and vice versa seamlessly“Neighboring” allows related papers

11、 in Medline, with similar subjects, and sequence entries, found through blast searches, to be grouped together08-Aug-22Text-Based Searching20Entrez at NCBI08-Aug-22Text-Based Searching21Entrez at NCBI08-Aug-22Text-Based Searching22Entrez at NCBI08-Aug-22Text-Based Searching23Entrez Pros and ConsPros

12、Integrates reference database with sequence database seamlesslyConsVery dependent on the network link as databases being searched are in the US08-Aug-22Text-Based Searching24GCG Software PackageSimilar syntax to Unix commands Write GCG in every new window to start the programSame principles for all

13、programs:Write command and argumentsChoose Parameters (default parameters)Receive an output (screen and file)08-Aug-22Text-Based Searching25Searching with GCGStringsearch: a simple text-search through local databases.Searching through definitions or through full annotations.The definitions contain a

14、 minimal amount of the information for each entry: accession, organism name, gene name, sequence length, date. 08-Aug-22Text-Based Searching26Searching with GCGThe annotations contain the complete documentation for each entry in the sequence database, including journal and author names, sequence fea

15、tures, comments, etc.Annotations take much longer to search through08-Aug-22Text-Based Searching27Getting a sequenceFetch: Get a sequence file to your account using the accession number or the id code.Example: fetch hum_hbbFetches all the files with the given accession number. Can be limited to a certain data base using database code:Example: fetch embl:u0161308-Aug-22Text-Based Searching28Se